Harvey Rubin has been following closely the creation of a new, more contagious form of H5N1 – the bird flu that’s killed about 400 people worldwide. He studies infectious diseases as part of Penn’s Institute for Strategic Threat Analysis and Response (ISTAR), which was set up after 9/11 to deal with issues of national security.

The normal version of the virus hasn’t yet become the terrifying pandemic some forecast because it doesn’t spread particularly easily from person to person. Most of the victims are thought to have contracted it directly from domestic birds. But now researchers at Ohio State University and the Netherlands have created a new form, mutated deliberately so it spreads easily between ferrets, an experimental animal whose reaction to the disease is thought to mirror our own.

What makes this modified H5N1 particularly dangerous is that in nature, viruses that become more contagious may also lose some of their lethal virulence, said Rubin. But this artificially mutated virus appears to be more virulent and more contagious.

That doesn’t mean scientists shouldn’t have made it, he said. “Knowing how this thing spreads is important science.” And a federal advisory panel known as The National Science Advisory Board for National Security in Bioscience was correct to tell scientific journals not to go public with the details of the creation of this super virus. “I think it’s a mistake to underestimate what a bad guy or a nut case could do,” he said.

Rubin said he advised that same panel back in the mid-1990s over similar concerns were raised over a project that deciphered the genetic sequences of the 1918 Spanish Flu, which killed millions of people. They decided to go ahead and publish the sequence, and so far no harm has come of it.

We’re lucky the dangerous bird flu virus H5N1 doesn’t spread easily from person to person – yet.  That could change thanks to the rapid pace of viral evolution. In trying to understand the course of potential evolution of H5N1, scientists in Ohio and the Netherlands modified the virus until they came across a version that does spread easily, according to news reports released yesterday. That’s important for scientists to know, but their work prompted an unprecedented move by the National Science Advisory Board for Biosecurity to request the recipe for making this virus be kept secret. The Washington Post and New York Times ran front page stories on this issue. Here’s how the Post story described the situation:

After weeks of reviewing papers describing the research, the NSABB said Tuesday it had recommended that the experiments’ “general conclusions” be published but not “details that could enable replication of the experiments by those who would seek to do harm.”

“Censorship is considered the ultimate sin of original research. However, we also have an imperative to keep certain research out of the hands of individuals who could use it for nefarious purposes,” said Michael T. Osterholm, a member of the board who is also director of the Center for Infectious Disease Research and Policy at the University of Minnesota. “It is not unexpected that these two things would clash in this very special situation.”

Big, gaseous planets are becoming a commonplace finding in our galaxy, but until now astronomers had never detected a body as small as our Earth orbiting another star. Two new planets announced today matter in the search for life because they are small enough to have a solid surface. They are too close to their sun to have liquid water, but astronomers are optimistic that more habitable worlds will be found soon.    

On Tuesday I caught up with Villanova astronomer Andrej Prsa, who was part of the team announcing the planets. They were detected with a space telescope called Kepler, launched in 2009 with the express goal of finding other earths.

Prsa’s job is to make sure Kepler is detecting real planets and not reacting to false alarms. The astronomers don’t actually see any of these planets but indirectly detect their presence by monitoring stars for tiny periodic dips in brightness. These dips are indications that planets are passing in front and creating mini-eclipses. (The image is an artist's reconstruction)

The newly announced planets only dim the stars by 100 parts per million, said Prsa, but measuring such minuscule changes is within Kepler’s ability.  The project has led to announcements of hundreds of “candidate planets,” he said, but astronomers have high standards of evidence when it comes to naming a true discovery.

To tell which candidates are real, the astronomers watch them for a few orbits to make sure the dimming really is periodic. And they have to rule out the possibility that they’re seeing the effects of a series of stars eclipsing each other.

Intriguing isn’t a word often associated with holiday decorations, but that’s the best way I can describe the Tree of Knowledge, created by Freethought Society founder Margaret Downey. Chester County commissioners have denied the society’s request to include it in a multi-cultural display alongside a Christmas tree, a menorah and other multicultural staples.

The tree’s current home is indoors at the Ethical Society near Rittenhouse Square.

At 9 feet tall, the Tree of Knowledge looks something like a Christmas tree, but it’s festooned with laminated jackets of books. It was impossible to resist walking around the tree to spot many books I'd loved and others I haven't read but should. Darwin’s “On the Origin of Species” had a nice spot in the front. The tree included other evolution-themed books written by Richard Dawkins and Stephen Jay Gould. There were also books by Carl Sagan, Bertrand Russell, Victor Stenger, Daniel Dennett and the much-missed Christopher Hitchens, who died last week at the age of 62.

The books are all supposed to be nontheist. A good fraction were science books. As a bookish child I would have been tranfixed and delighted by a tree like this.

The Freethought Society is still collecting laminated book covers to add to next year’s tree. To me the most notable omissions were “Letters from Earth” by Mark Twain, “Farenheit 451” by Ray Bradbury, and anything by physicist Richard Feynman.

Biologists agree on the big picture when it comes to Darwinian evolution, but they're still working out many details. One longstanding puzzle is why there's so much variation from person to person, why some people like broccoli, for example, and others hate it.

There's evidence that people who hate broccoli are not being childish or stubborn. Some broccoli haters are reacting to compounds called glucosinolates, which are also present in brussels sprouts and other so-called cruciferous vegetables.

Some people taste these as intolerably bitter, and others can't taste them at all. The difference is genetic. The gene responsible, called hTAS2R38, comes in several forms, some of which enable people to detect this stuff.

NOTE TO READERS: Thank you all for making intelligent comments on this blog entry. It's wonderful for me to see the level of discussion here. Unfortunately I am not in charge of the comments. I'm not the one who decides to block them. I do know that overly long comments can be rejected. If you have a plus-sized comment please feel free to email it directly to me at fflam@phillynews.com, and I can use it in the blog to generate a new discussion. You can also break up long comments into several consecutive parts. I apologize for the inconvenience. Don't give up! We need rational discourse at newspaper websites. Faye

Jack Szostak is a Harvard biologist who won a Nobel Prize for physiology or medicine and is devoting his time to understanding the origin of life. He has been public about the importance of evolution to biology. So how could he have been quoted supporting a creationist view and undercutting his own scientific quest?

Szostak's seemingly pro-creationist quote appeared in a piece by a rabbi, Moshe Averick. It appeared on a website called Algemeiner, and the sole purpose seemed to be to attack evolutionary biologist and science popularizer Jerry Coyne. I found the piece from a link on Coyne's blog, which is called Why Evolution is True.

Averick tried to support his attack with a quote by Szostak. To creationists, it must have  looked like a nice piece of ammunition – a biologist and Nobel winner supporting the need for some kind of intelligent design to get life started:

“It is virtually impossible to imagine how a cell’s machines…could have formed spontaneously from non-living matter,” is because it is impossible for a cell’s machines to have formed spontaneously from non-living matter. The notion that the functional complexity of a bacterium could be the result of an unguided process is as absurd as asserting that the sculptures on Mt. Rushmore were the result of an unguided, naturalistic process

I didn't choose my own sexual orientation, but apparently some Inquire readers did. I learned this from the responses I received following Monday’s column, which had the term “gay gene” in the headline but was not really about gay genes.

It was about a meeting that dealt with newer research on the biology of sexual orientation. Most of the column was devoted to a theory that male sexual orientation can be influenced during development by the actions of the mother’s immune system.

This reader seems to have missed this point:

Faye Flam's article on the gay gene is a classic example of people using science to attempt to justify what they are already determined to believe. The "evidence" provided includes the well-known Hamer study, which, as the article acknowledged, has never been successfully replicated, and a twin study that showed that, when one member of a pair of identical twins was gay, the other also was gay 50% of the time. If homosexuality is genetic, wouldn't that number have been 100%? Wouldn't environmental factors provide a more logical explanation for that finding? The remainder of the article consists of a series of speculations about what "might" have allowed homosexuality to survive the pitiless weeding-out process known as natural selection. These are tenuous foundations indeed on which to attempt to convince people that homosexual behavior is justifiable because it is not a matter of personal choice, but clearly anything that contradicts the orthodoxy of the moment, whether scientific or biblical, must be twisted or rejected.

I guess he didn’t grasp the point made by Toronto psychiatrist Ray Blanchard about the influence of the environment – in particular the prenatal environment – in influencing sexual orientation. Sexual orientation does seem to be shaped by a combination of genetic and biological factors.

Body Hair is one of those enduring mysteries of evolution.  Some scientists write papers about why we have hair, and others write about why we don’t have more of it. Since other apes are furrier than we are (well, most of us), it’s a natural assumption that we lost much of our body hair somewhere along the line. This latest hypothesis for the retention of body hair appeared in the journal Biology Letters, and was summarized here in Science:

"When it creeps into your bed at night and crawls across your skin, the bedbug (inset) has to navigate a forest of body hair before plunging its proboscis into your flesh for a meal. One wrong step, and it could get smushed. Tickled by the question of how people detect such microscopic pests, researchers recruited 19 volunteers with various amounts of body hair and shaved one of each of their arms. They then asked the subjects to look away while they dropped bedbugs onto their arms. The volunteers hit a button as soon as they felt something crawling on them. Participants, especially men, with more hair follicles per square inch and whose body hairs were longer, tended to be several seconds quicker than less hirsute individuals to notice the bugs on their unshaven arms, the researchers report online today in Biology Letters. And everyone took a long time to notice the bedbugs on the shaved arm. That might explain why humans still have hair on their bodies, the researchers conclude, since we no longer need it for keeping warm."

I hope they paid these volunteers well. This paper demonstrates a possible advantage of having body hair, but that doesn’t mean the need for bug protection was the reason people retained some hair. There are many unanswered questions here. If body hair evolved to warn us about insects, why are some of us much more naked than others? Why do men vary from smooth to furry?  

The study doesn’t explain why men are hairier than women, at least on average. When there’s a significant sex difference in a trait, some scientists suspect a phenomenon known as sexual selection. This is, roughly, the selective propagation of traits that incite the desire of the opposite sex. Could male body hair variation have been shaped by the varying regional tastes of women?

The bug detection idea also doesn’t explain why we have hair where we have it. I could see why you’d want to be extra safe in keeping bedbugs and the like away from your pubic zone, but is there some reason all of us need extra warning in our armpits?

Today scientists revealed the first major results from the biggest, most elaborate scientific apparatus ever built – the Large Hadron Collider in Europe. True to predictions, they reported hints of a long-sought particle called the Higgs. You can read more in this news story. I worked really hard on this story. I talked to all kinds of people and hung out with the physicists at Penn, but my story won't get on the front page because I refuse to use the god-awful term "God particle".  

Physicist don't call the Higgs the God particle.  That “nickname” comes from the title of a 1993 book by Nobel winning physicist Leon Lederman. Lederman took a lot of criticism for calling his book, “The God Particle.” (though it was undoubtedly good for sales)

As part of my research for my story I read a more recent book on the Higgs search, Massive, by British journalist Ian Sample. It's very readable and informative, and he does a great job of weaving together current science and history, but what I found a little weird was that in one of the editions of his book, he used the subtitle, "The Search for the God Particle," and yet he has this to say about Lederman’s abuse of the Lord's name:

“The nickname ranks as one of the most, if not them most, derided in the history of physics. Working scientists rant aloud about how profoundly dreadful a name it is. Some say it is just plain lame.”

Since then Lederman has been quoted saying he now realizes that title offended two groups of people – those who believe in God and those who don’t believe in God.